We recommend analyzing cortical data on surface representations, and this
is reflected in the formats we use for our released data, so files ending
in .nii.gz will generally not contain useful ROIs for this purpose, as they
are volume files.
We have cifti label
files,
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.BA.32k_fs_LR.dlabel.nii
, which contain labels 4a and 4p (named "L_BA4a" and similar), derived from
freesurfer probability maps. You can turn the labels into binary ROIs with
the command -cifti-label-to-roi:
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-label-to-roi
Where you go from there depends on what software or language you intend to
use and what you want to do with them - you can read them into
matlab/octave, separate the cifti files into single-hemisphere gifti files,
etc.
Tim
On Mon, Jul 27, 2015 at 11:22 AM, Philip Henningsen <
[email protected]> wrote:
> Hi
>
> I'm doing a project on the motor task and in relation to this, I would
> like to extract all the activation values for both the left and right motor
> cortex. I'm not sure how I should approach this, however. Which files
> contains the ROIs exactly? I have tried reading both the manual, appendix
> III, and the FAQ, but the amount of different files and folders continue to
> perplex me.
>
> To begin with I simply looked in the ROIs folder within MNINonLinear for a
> subject. This contains four files: Atlas_ROIs.2.nii.gz,
> Atlas_wmparc.2.nii.gz ROIs.2.nii.gz, and wmparc.2.nii.gz. They all seem
> to have the same shape as the functional images, which made me hope they
> were simply a map of which voxels belonged to which ROIs. If this is true,
> I still need a list of ROI -> index, but I have no idea if my assumption is
> even true.
>
> Is there a simple way to extract a specific ROI?
>
> Best regards
>
> Philip
>
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>
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